CVS commit: pkgsrc/biology/py-biopython

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/py-biopython
From: "Adam Ciarcinski" <adam%netbsd.org@localhost>
Date: Mon, 10 Feb 2025 13:08:29 +0000

Module Name:    pkgsrc
Committed By:   adam
Date:           Mon Feb 10 13:08:29 UTC 2025

Modified Files:
        pkgsrc/biology/py-biopython: Makefile PLIST distinfo

Log Message:
py-biopython: updated to 1.85

Biopython 1.85

This release of Biopython supports Python 3.9, 3.10, 3.11, 3.12 and 3.13. It
has also been tested on PyPy3.9 v7.3.13. Python 3.9 is approaching end of
life, our support for it is now deprecated.

Some optimisation work was done for ``Bio.SeqIO`` including avoiding nested
iterators, and speeding up both FASTA and FASTQ parsing.

``Bio.motifs`` now supports reading PFM from Cys2His2 Zinc Finger Proteins PWM
Predictor and reading motifs in ``pfm-four-columns`` format will set motif name
to "" instead of None, when no motif name was found.

Tests that use assertAlmostEqual calls now use ``places`` parameter with enough
presision when comparing very small numbers in scientific notation.

``Bio.motifs`` now supports reverse complementing RNA motifs and correctly
generating degenerate consensus sequences for RNA motifs.

``Bio.motifs.minimal`` now supports parsing RNA motifs and parsing motifs
for which not all statistics are provided (e.g. missing E-values or nsites).

``Bio.motifs.clusterbuster`` now supports parsing GAP and WEIGHT parameters
and can optionally write Cluster Buster motif files with floats instead of
integers, by specifying the ``precision=<int>`` parameter when writing:
e.g. motifs.write(motifs, "clusterbuster", precision=2)

Additionally, a number of small bugs and typos have been fixed with additions
to the test suite and type annotations.


To generate a diff of this commit:
cvs rdiff -u -r1.14 -r1.15 pkgsrc/biology/py-biopython/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/py-biopython/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/py-biopython/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/py-biopython/Makefile
diff -u pkgsrc/biology/py-biopython/Makefile:1.14 pkgsrc/biology/py-biopython/Makefile:1.15
--- pkgsrc/biology/py-biopython/Makefile:1.14   Mon Nov 11 07:27:52 2024
+++ pkgsrc/biology/py-biopython/Makefile        Mon Feb 10 13:08:29 2025
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.14 2024/11/11 07:27:52 wiz Exp $
+# $NetBSD: Makefile,v 1.15 2025/02/10 13:08:29 adam Exp $
 
-DISTNAME=      biopython-1.81
+DISTNAME=      biopython-1.85
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-CATEGORIES=    biology
+CATEGORIES=    biology python
 MASTER_SITES=  http://biopython.org/DIST/
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
@@ -12,15 +12,6 @@ LICENSE=     biopython
 
 TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools-[0-9]*:../../devel/py-setuptools
 
-USE_TOOLS+=    pax
-
-INSTALLATION_DIRS+=    share/doc/biopython-${PYVERSSUFFIX} share/examples/biopython-${PYVERSSUFFIX}
-
-post-install:
-       ${INSTALL_DATA} ${WRKSRC}/README.rst ${DESTDIR}${PREFIX}/share/doc/biopython-${PYVERSSUFFIX}
-       ${INSTALL_DATA} ${WRKSRC}/Doc/Tutorial.pdf ${DESTDIR}${PREFIX}/share/doc/biopython-${PYVERSSUFFIX}
-       cd ${WRKSRC}/Doc/examples && ${PAX} -rw . ${DESTDIR}${PREFIX}/share/examples/biopython-${PYVERSSUFFIX}
-
 .include "../../lang/python/wheel.mk"
 .include "../../math/py-numpy/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/py-biopython/PLIST
diff -u pkgsrc/biology/py-biopython/PLIST:1.3 pkgsrc/biology/py-biopython/PLIST:1.4
--- pkgsrc/biology/py-biopython/PLIST:1.3       Sun Nov  5 23:52:20 2023
+++ pkgsrc/biology/py-biopython/PLIST   Mon Feb 10 13:08:29 2025
@@ -1,4 +1,10 @@
-@comment $NetBSD: PLIST,v 1.3 2023/11/05 23:52:20 wiz Exp $
+@comment $NetBSD: PLIST,v 1.4 2025/02/10 13:08:29 adam Exp $
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.rst
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/Bio/Affy/CelFile.py
 ${PYSITELIB}/Bio/Affy/CelFile.pyc
 ${PYSITELIB}/Bio/Affy/CelFile.pyo
@@ -41,11 +47,18 @@ ${PYSITELIB}/Bio/Align/Applications/__in
 ${PYSITELIB}/Bio/Align/__init__.py
 ${PYSITELIB}/Bio/Align/__init__.pyc
 ${PYSITELIB}/Bio/Align/__init__.pyo
-${PYSITELIB}/Bio/Align/_aligners.c
-${PYSITELIB}/Bio/Align/_aligners.so
+${PYSITELIB}/Bio/Align/_aligncore.c
+${PYSITELIB}/Bio/Align/_aligncore.so
+${PYSITELIB}/Bio/Align/_codonaligner.c
+${PYSITELIB}/Bio/Align/_codonaligner.so
+${PYSITELIB}/Bio/Align/_pairwisealigner.c
+${PYSITELIB}/Bio/Align/_pairwisealigner.so
 ${PYSITELIB}/Bio/Align/a2m.py
 ${PYSITELIB}/Bio/Align/a2m.pyc
 ${PYSITELIB}/Bio/Align/a2m.pyo
+${PYSITELIB}/Bio/Align/analysis.py
+${PYSITELIB}/Bio/Align/analysis.pyc
+${PYSITELIB}/Bio/Align/analysis.pyo
 ${PYSITELIB}/Bio/Align/bed.py
 ${PYSITELIB}/Bio/Align/bed.pyc
 ${PYSITELIB}/Bio/Align/bed.pyo
@@ -58,6 +71,9 @@ ${PYSITELIB}/Bio/Align/bigmaf.pyo
 ${PYSITELIB}/Bio/Align/bigpsl.py
 ${PYSITELIB}/Bio/Align/bigpsl.pyc
 ${PYSITELIB}/Bio/Align/bigpsl.pyo
+${PYSITELIB}/Bio/Align/chain.py
+${PYSITELIB}/Bio/Align/chain.pyc
+${PYSITELIB}/Bio/Align/chain.pyo
 ${PYSITELIB}/Bio/Align/clustal.py
 ${PYSITELIB}/Bio/Align/clustal.pyc
 ${PYSITELIB}/Bio/Align/clustal.pyo
@@ -184,15 +200,15 @@ ${PYSITELIB}/Bio/Blast/NCBIWWW.pyo
 ${PYSITELIB}/Bio/Blast/NCBIXML.py
 ${PYSITELIB}/Bio/Blast/NCBIXML.pyc
 ${PYSITELIB}/Bio/Blast/NCBIXML.pyo
-${PYSITELIB}/Bio/Blast/ParseBlastTable.py
-${PYSITELIB}/Bio/Blast/ParseBlastTable.pyc
-${PYSITELIB}/Bio/Blast/ParseBlastTable.pyo
-${PYSITELIB}/Bio/Blast/Record.py
-${PYSITELIB}/Bio/Blast/Record.pyc
-${PYSITELIB}/Bio/Blast/Record.pyo
 ${PYSITELIB}/Bio/Blast/__init__.py
 ${PYSITELIB}/Bio/Blast/__init__.pyc
 ${PYSITELIB}/Bio/Blast/__init__.pyo
+${PYSITELIB}/Bio/Blast/_parser.py
+${PYSITELIB}/Bio/Blast/_parser.pyc
+${PYSITELIB}/Bio/Blast/_parser.pyo
+${PYSITELIB}/Bio/Blast/_writers.py
+${PYSITELIB}/Bio/Blast/_writers.pyc
+${PYSITELIB}/Bio/Blast/_writers.pyo
 ${PYSITELIB}/Bio/CAPS/__init__.py
 ${PYSITELIB}/Bio/CAPS/__init__.pyc
 ${PYSITELIB}/Bio/CAPS/__init__.pyo
@@ -215,9 +231,6 @@ ${PYSITELIB}/Bio/Data/IUPACData.pyo
 ${PYSITELIB}/Bio/Data/PDBData.py
 ${PYSITELIB}/Bio/Data/PDBData.pyc
 ${PYSITELIB}/Bio/Data/PDBData.pyo
-${PYSITELIB}/Bio/Data/SCOPData.py
-${PYSITELIB}/Bio/Data/SCOPData.pyc
-${PYSITELIB}/Bio/Data/SCOPData.pyo
 ${PYSITELIB}/Bio/Data/__init__.py
 ${PYSITELIB}/Bio/Data/__init__.pyc
 ${PYSITELIB}/Bio/Data/__init__.pyo
@@ -435,6 +448,7 @@ ${PYSITELIB}/Bio/Entrez/DTDs/elink_02012
 ${PYSITELIB}/Bio/Entrez/DTDs/epost.dtd
 ${PYSITELIB}/Bio/Entrez/DTDs/esearch.dtd
 ${PYSITELIB}/Bio/Entrez/DTDs/esummary-v1.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/esummary_clinvar.dtd
 ${PYSITELIB}/Bio/Entrez/DTDs/esummary_gene.dtd
 ${PYSITELIB}/Bio/Entrez/DTDs/format.ent
 ${PYSITELIB}/Bio/Entrez/DTDs/htmltable.dtd
@@ -524,6 +538,8 @@ ${PYSITELIB}/Bio/Entrez/Parser.py
 ${PYSITELIB}/Bio/Entrez/Parser.pyc
 ${PYSITELIB}/Bio/Entrez/Parser.pyo
 ${PYSITELIB}/Bio/Entrez/XSDs/IPGReportSet.xsd
+${PYSITELIB}/Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd
+${PYSITELIB}/Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd
 ${PYSITELIB}/Bio/Entrez/__init__.py
 ${PYSITELIB}/Bio/Entrez/__init__.pyc
 ${PYSITELIB}/Bio/Entrez/__init__.pyo
@@ -754,6 +770,9 @@ ${PYSITELIB}/Bio/PDB/PDBIO.pyo
 ${PYSITELIB}/Bio/PDB/PDBList.py
 ${PYSITELIB}/Bio/PDB/PDBList.pyc
 ${PYSITELIB}/Bio/PDB/PDBList.pyo
+${PYSITELIB}/Bio/PDB/PDBMLParser.py
+${PYSITELIB}/Bio/PDB/PDBMLParser.pyc
+${PYSITELIB}/Bio/PDB/PDBMLParser.pyo
 ${PYSITELIB}/Bio/PDB/PDBParser.py
 ${PYSITELIB}/Bio/PDB/PDBParser.pyc
 ${PYSITELIB}/Bio/PDB/PDBParser.pyo
@@ -766,11 +785,6 @@ ${PYSITELIB}/Bio/PDB/PSEA.pyo
 ${PYSITELIB}/Bio/PDB/Polypeptide.py
 ${PYSITELIB}/Bio/PDB/Polypeptide.pyc
 ${PYSITELIB}/Bio/PDB/Polypeptide.pyo
-${PYSITELIB}/Bio/PDB/QCPSuperimposer/__init__.py
-${PYSITELIB}/Bio/PDB/QCPSuperimposer/__init__.pyc
-${PYSITELIB}/Bio/PDB/QCPSuperimposer/__init__.pyo
-${PYSITELIB}/Bio/PDB/QCPSuperimposer/qcprotmodule.c
-${PYSITELIB}/Bio/PDB/QCPSuperimposer/qcprotmodule.so
 ${PYSITELIB}/Bio/PDB/Residue.py
 ${PYSITELIB}/Bio/PDB/Residue.pyc
 ${PYSITELIB}/Bio/PDB/Residue.pyo
@@ -801,6 +815,14 @@ ${PYSITELIB}/Bio/PDB/Superimposer.pyo
 ${PYSITELIB}/Bio/PDB/__init__.py
 ${PYSITELIB}/Bio/PDB/__init__.pyc
 ${PYSITELIB}/Bio/PDB/__init__.pyo
+${PYSITELIB}/Bio/PDB/_bcif_helper.so
+${PYSITELIB}/Bio/PDB/alphafold_db.py
+${PYSITELIB}/Bio/PDB/alphafold_db.pyc
+${PYSITELIB}/Bio/PDB/alphafold_db.pyo
+${PYSITELIB}/Bio/PDB/bcifhelpermodule.c
+${PYSITELIB}/Bio/PDB/binary_cif.py
+${PYSITELIB}/Bio/PDB/binary_cif.pyc
+${PYSITELIB}/Bio/PDB/binary_cif.pyo
 ${PYSITELIB}/Bio/PDB/ccealign.so
 ${PYSITELIB}/Bio/PDB/ccealignmodule.c
 ${PYSITELIB}/Bio/PDB/cealign.py
@@ -997,9 +1019,6 @@ ${PYSITELIB}/Bio/SearchIO/BlastIO/__init
 ${PYSITELIB}/Bio/SearchIO/BlastIO/blast_tab.py
 ${PYSITELIB}/Bio/SearchIO/BlastIO/blast_tab.pyc
 ${PYSITELIB}/Bio/SearchIO/BlastIO/blast_tab.pyo
-${PYSITELIB}/Bio/SearchIO/BlastIO/blast_text.py
-${PYSITELIB}/Bio/SearchIO/BlastIO/blast_text.pyc
-${PYSITELIB}/Bio/SearchIO/BlastIO/blast_text.pyo
 ${PYSITELIB}/Bio/SearchIO/BlastIO/blast_xml.py
 ${PYSITELIB}/Bio/SearchIO/BlastIO/blast_xml.pyc
 ${PYSITELIB}/Bio/SearchIO/BlastIO/blast_xml.pyo
@@ -1060,15 +1079,6 @@ ${PYSITELIB}/Bio/SearchIO/__init__.pyo
 ${PYSITELIB}/Bio/SearchIO/_index.py
 ${PYSITELIB}/Bio/SearchIO/_index.pyc
 ${PYSITELIB}/Bio/SearchIO/_index.pyo
-${PYSITELIB}/Bio/SearchIO/_legacy/NCBIStandalone.py
-${PYSITELIB}/Bio/SearchIO/_legacy/NCBIStandalone.pyc
-${PYSITELIB}/Bio/SearchIO/_legacy/NCBIStandalone.pyo
-${PYSITELIB}/Bio/SearchIO/_legacy/ParserSupport.py
-${PYSITELIB}/Bio/SearchIO/_legacy/ParserSupport.pyc
-${PYSITELIB}/Bio/SearchIO/_legacy/ParserSupport.pyo
-${PYSITELIB}/Bio/SearchIO/_legacy/__init__.py
-${PYSITELIB}/Bio/SearchIO/_legacy/__init__.pyc
-${PYSITELIB}/Bio/SearchIO/_legacy/__init__.pyo
 ${PYSITELIB}/Bio/SearchIO/_model/__init__.py
 ${PYSITELIB}/Bio/SearchIO/_model/__init__.pyc
 ${PYSITELIB}/Bio/SearchIO/_model/__init__.pyo
@@ -1105,6 +1115,9 @@ ${PYSITELIB}/Bio/SeqIO/FastaIO.pyo
 ${PYSITELIB}/Bio/SeqIO/GckIO.py
 ${PYSITELIB}/Bio/SeqIO/GckIO.pyc
 ${PYSITELIB}/Bio/SeqIO/GckIO.pyo
+${PYSITELIB}/Bio/SeqIO/GfaIO.py
+${PYSITELIB}/Bio/SeqIO/GfaIO.pyc
+${PYSITELIB}/Bio/SeqIO/GfaIO.pyo
 ${PYSITELIB}/Bio/SeqIO/IgIO.py
 ${PYSITELIB}/Bio/SeqIO/IgIO.pyc
 ${PYSITELIB}/Bio/SeqIO/IgIO.pyo
@@ -1167,12 +1180,6 @@ ${PYSITELIB}/Bio/SeqRecord.pyo
 ${PYSITELIB}/Bio/SeqUtils/CheckSum.py
 ${PYSITELIB}/Bio/SeqUtils/CheckSum.pyc
 ${PYSITELIB}/Bio/SeqUtils/CheckSum.pyo
-${PYSITELIB}/Bio/SeqUtils/CodonUsage.py
-${PYSITELIB}/Bio/SeqUtils/CodonUsage.pyc
-${PYSITELIB}/Bio/SeqUtils/CodonUsage.pyo
-${PYSITELIB}/Bio/SeqUtils/CodonUsageIndices.py
-${PYSITELIB}/Bio/SeqUtils/CodonUsageIndices.pyc
-${PYSITELIB}/Bio/SeqUtils/CodonUsageIndices.pyo
 ${PYSITELIB}/Bio/SeqUtils/IsoelectricPoint.py
 ${PYSITELIB}/Bio/SeqUtils/IsoelectricPoint.pyc
 ${PYSITELIB}/Bio/SeqUtils/IsoelectricPoint.pyo
@@ -1230,15 +1237,6 @@ ${PYSITELIB}/Bio/UniProt/GOA.pyo
 ${PYSITELIB}/Bio/UniProt/__init__.py
 ${PYSITELIB}/Bio/UniProt/__init__.pyc
 ${PYSITELIB}/Bio/UniProt/__init__.pyo
-${PYSITELIB}/Bio/Wise/__init__.py
-${PYSITELIB}/Bio/Wise/__init__.pyc
-${PYSITELIB}/Bio/Wise/__init__.pyo
-${PYSITELIB}/Bio/Wise/dnal.py
-${PYSITELIB}/Bio/Wise/dnal.pyc
-${PYSITELIB}/Bio/Wise/dnal.pyo
-${PYSITELIB}/Bio/Wise/psw.py
-${PYSITELIB}/Bio/Wise/psw.pyc
-${PYSITELIB}/Bio/Wise/psw.pyo
 ${PYSITELIB}/Bio/__init__.py
 ${PYSITELIB}/Bio/__init__.pyc
 ${PYSITELIB}/Bio/__init__.pyo
@@ -1321,6 +1319,7 @@ ${PYSITELIB}/Bio/phenotype/phen_micro.py
 ${PYSITELIB}/Bio/phenotype/pm_fitting.py
 ${PYSITELIB}/Bio/phenotype/pm_fitting.pyc
 ${PYSITELIB}/Bio/phenotype/pm_fitting.pyo
+${PYSITELIB}/Bio/py.typed
 ${PYSITELIB}/BioSQL/BioSeq.py
 ${PYSITELIB}/BioSQL/BioSeq.pyc
 ${PYSITELIB}/BioSQL/BioSeq.pyo
@@ -1336,37 +1335,4 @@ ${PYSITELIB}/BioSQL/Loader.pyo
 ${PYSITELIB}/BioSQL/__init__.py
 ${PYSITELIB}/BioSQL/__init__.pyc
 ${PYSITELIB}/BioSQL/__init__.pyo
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
-${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.rst
-${PYSITELIB}/${WHEEL_INFODIR}/METADATA
-${PYSITELIB}/${WHEEL_INFODIR}/RECORD
-${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
-${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
-share/doc/biopython-${PYVERSSUFFIX}/README.rst
-share/doc/biopython-${PYVERSSUFFIX}/Tutorial.pdf
-share/examples/biopython-${PYVERSSUFFIX}/ACT_example.py
-share/examples/biopython-${PYVERSSUFFIX}/PF05371_seed.sth
-share/examples/biopython-${PYVERSSUFFIX}/Plates.csv
-share/examples/biopython-${PYVERSSUFFIX}/Proux_et_al_2002_Figure_6.py
-share/examples/biopython-${PYVERSSUFFIX}/alpha.faa
-share/examples/biopython-${PYVERSSUFFIX}/beta.faa
-share/examples/biopython-${PYVERSSUFFIX}/clustal_run.py
-share/examples/biopython-${PYVERSSUFFIX}/ec_5.4.2.2.txt
-share/examples/biopython-${PYVERSSUFFIX}/fasta_dictionary.py
-share/examples/biopython-${PYVERSSUFFIX}/fasta_iterator.py
-share/examples/biopython-${PYVERSSUFFIX}/ls_orchid.fasta
-share/examples/biopython-${PYVERSSUFFIX}/ls_orchid.gbk
-share/examples/biopython-${PYVERSSUFFIX}/ls_orchid.gbk.bgz
-share/examples/biopython-${PYVERSSUFFIX}/ls_orchid.gbk.bz2
-share/examples/biopython-${PYVERSSUFFIX}/ls_orchid.gbk.gz
-share/examples/biopython-${PYVERSSUFFIX}/m_cold.fasta
-share/examples/biopython-${PYVERSSUFFIX}/my_blast.xml
-share/examples/biopython-${PYVERSSUFFIX}/my_blat.psl
-share/examples/biopython-${PYVERSSUFFIX}/nmr/noed.xpk
-share/examples/biopython-${PYVERSSUFFIX}/nmr/simplepredict.py
-share/examples/biopython-${PYVERSSUFFIX}/opuntia.aln
-share/examples/biopython-${PYVERSSUFFIX}/opuntia.dnd
-share/examples/biopython-${PYVERSSUFFIX}/opuntia.fasta
-share/examples/biopython-${PYVERSSUFFIX}/simple.dnd
-share/examples/biopython-${PYVERSSUFFIX}/swissprot.py
-share/examples/biopython-${PYVERSSUFFIX}/www_blast.py
+${PYSITELIB}/BioSQL/py.typed

Index: pkgsrc/biology/py-biopython/distinfo
diff -u pkgsrc/biology/py-biopython/distinfo:1.5 pkgsrc/biology/py-biopython/distinfo:1.6
--- pkgsrc/biology/py-biopython/distinfo:1.5    Sun Nov  5 23:52:20 2023
+++ pkgsrc/biology/py-biopython/distinfo        Mon Feb 10 13:08:29 2025
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.5 2023/11/05 23:52:20 wiz Exp $
+$NetBSD: distinfo,v 1.6 2025/02/10 13:08:29 adam Exp $
 
-BLAKE2s (biopython-1.81.tar.gz) = dbd9c3cab115b2b20dd320fd20e2c686681cbef4381d758b291b5643e9ba86ef
-SHA512 (biopython-1.81.tar.gz) = 1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed
-Size (biopython-1.81.tar.gz) = 19324875 bytes
+BLAKE2s (biopython-1.85.tar.gz) = 07d6d61b98237e867ee25289b4588ea78d58d4a45623b2fdb4bbca31487ba5f9
+SHA512 (biopython-1.85.tar.gz) = a9bff4fdf34f71f74f35a9bbf25887d6fcf84622d77854e11b0da418b6ff88c7d6e49474d82ca2e4da782ea07cc28f03b43b219b798a806ab02e11af21cd9dab
+Size (biopython-1.85.tar.gz) = 19909902 bytes

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